tests-linux.yml

name: Tests Linux (Low Memory)

on:
  workflow_dispatch:
  pull_request:
    branches:
      - dev
      - master
  push:
    branches:
      - dev
      - master

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      # Limit concurrency to reduce memory pressure
      max-parallel: 2
      matrix:
        python-version: ["3.10", "3.11", "3.12"]
    timeout-minutes: 60

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Display Python version
        run: python -c "import sys; print(sys.version)"

      - name: Install minimal system dependencies
        run: |
          sudo apt-get update -qq
          sudo apt-get install -y --no-install-recommends openslide-tools pandoc
          sudo apt-get clean
          sudo rm -rf /var/lib/apt/lists/*

      - name: Set up Micromamba (cached)
        uses: mamba-org/setup-micromamba@v2
        with:
          micromamba-version: "1.5.6-0"
          environment-name: pathml
          environment-file: requirements/environment_test.yml
          init-shell: bash
          cache-environment: true
          create-args: >-
            python=${{ matrix.python-version }}
        env:
          MAMBA_NO_BANNER: 1

      - name: Show environment info
        run: |
          micromamba info
          micromamba list | head -n 20
          df -h

      - name: Set default Temurin JDK 17
        run: |
          sudo update-java-alternatives --set temurin-17-jdk-amd64 || true
          java -version

      - name: Install PathML (editable)
        shell: bash -l {0}
        run: pip install -e .

      - name: Install lightweight torchvision
        shell: bash -l {0}
        run: pip install torchvision==0.23.0 --no-cache-dir

      - name: Aggressive disk cleanup
        run: |
          echo "Freeing disk space..."
          sudo swapoff -a || true
          sudo rm -f /swapfile || true
          docker system prune -af || true
          sudo apt-get clean
          sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc || true
          df -h

      - name: Fix coverage-numba incompatibility
        shell: bash -l {0}
        run: |
          micromamba activate pathml
          pip install "numpy>=1.26,<2" "coverage>=7.4,<8" "numba>=0.60,<0.62" --force-reinstall --no-cache-dir
          python -m coverage --version
          python -c "import numba; print('Numba version:', numba.__version__)"

      - name: Test other modules with pytest and generate coverage
        shell: bash -l {0}
        run: |
          COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"

      - name: Test tile_stitcher with pytest and generate coverage
        shell: bash -l {0}
        run: |
          COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py

      - name: Combine Coverage Data
        shell: bash -l {0}
        run: |
          coverage combine .coverage_tilestitcher .coverage_others

      - name: Generate Combined Coverage Report
        shell: bash -l {0}
        run: |
          coverage xml -o combined_coverage.xml

      - name: Upload combined coverage to Codecov
        uses: codecov/codecov-action@v2
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          env_vars: OS,PYTHON
          fail_ci_if_error: true
          files: ./combined_coverage.xml
          name: codecov-umbrella
          verbose: true

      - name: Compile docs
        shell: bash -l {0}
        run: |
          cd docs
          pip install -r readthedocs-requirements.txt
          make html